Maryland’s four historically black universities are likely to gain more distinctive programs to compete for students following a federal ruling that the state has allowed too much academic overlap among its public universities, tilting the market in favor of traditionally white institutions.

The ruling Monday from U.S. District Judge Catherine C. Blake was a partial but significant victory for plaintiffs who sued the state in 2006 on behalf of students from the historically black Morgan State, Bowie State and Coppin State universities and the University of Maryland Eastern Shore. The case was tried in Baltimore in 2012.

Blake ruled that state policies and practices of “unnecessary program duplication” have “segregative effects,” perpetuating imbalances that linger from the era when Maryland ran a dual system of public higher education: one track for students who were white and an inferior one for those who were black. Blake ruled that the state must remedy the problem.

By the numbers, the judge boiled the case down to this: The state’s traditionally white institutions, or TWIs, have an average of 42 “unique, non-core” academic programs each. The historically black institutions, or HBIs, have an average of 11 apiece.

Analyzing unique programs deemed in high demand, the judge found there are 17 per TWI and three per HBI.

Unique academic programs are highly prized among universities. They tend to be a magnet for students of all backgrounds, and they give universities a talking point in recruiting. Duplication, on the other hand, can hurt some universities that are struggling to raise enrollment, revenue and prestige.

“The state offered no evidence that it has made any serious effort to address continuing historic duplication,” Blake wrote in her 60-page ruling.

She cited the example of a master’s degree program in computer science at Bowie State, which was offered before traditionally white Towson University started such a program. Enrollment in Bowie State’s program fell from 119 students in 1994 to 29 in 2008. It rose in Towson’s version from 23 in 1994 to 101 in 2008. Likewise, enrollment in master’s programs for teaching at Bowie State, Coppin State and Morgan State fell after the University of Maryland Baltimore County began offering such a program.

The judge’s ruling was nuanced. She wrote that the state has made “great progress in recognizing and attempting to rectify those wrongs” from the era of legal segregation. She also upheld the state’s funding formula for higher education, dismissing an argument from plaintiffs that the system for distributing money discriminates against the historically black universities.

Plaintiffs said they were elated.

“We sought to prevent the marginalization of the HBIs and wanted them to have academic programs that are attractive to students and properly supported by faculty, facilities and other resources,” David Burton, of the Coalition for Excellence and Equity in Maryland Higher Education, said in a statement.

The plaintiffs had alleged violations of federal civil rights law and the equal protection clause of the 14th Amendment.

The primary defendant in the case is the Maryland Higher Education Commission, which sets state policy.

A spokeswoman for Gov. Martin O’Malley (D), Samantha Kappalman, said: “We are pleased, though not surprised, that the court recognized our commitment to provide access to quality public colleges and universities for all Marylanders. In particular, the court noted that the investments we make in both the capital and operating budgets for institutions of higher education are fair.”

She added: “[W]e respectfully disagree with the court’s conclusions regarding duplication. We are continuing to review [the] decision and are considering all of our options, including resolving the lone remaining issue through constructive mediation.”

Blake, in the ruling, wrote that the court “strongly suggests” mediation, but she warned that “further proceedings” in the case could be necessary if talks are unsuccessful.

There are 13 public colleges and universities in Maryland, led by the flagship University of Maryland at College Park.

The others that are not historically black are the University of Maryland at Baltimore, the University of Maryland Baltimore County, the University of Maryland University College, the University of Baltimore, Frostburg State University, Salisbury University, Towson University and St. Mary’s College of Maryland.

As a result of the ruling, the historically black universities will gain leverage in what is a continual debate within the state over which programs should be located at which schools. The issue resonates strongly in the Baltimore metropolitan area, which has numerous public universities. In 2005, when the University of Baltimore and Towson developed a joint master’s in business administration degree, Morgan State objected that the new offering would needlessly duplicate its own MBA program.

Morgan State President David Wilson hailed the ruling, saying that it will propel discussions of how to enhance his university. That might fuel proposals for programs in environmental sustainability, cybersecurity and nanotechnology, for a school of public health or for a law school, he said.

“This is going to enhance tremendously the vision that we have for Morgan as a major urban research university, with a comprehensive menu of doctoral programs, with high-demand programs, with competitive professional schools,” Wilson said.

Nick Anderson covers higher education for The Washington Post. He has been a writer and editor at The Post since 2005.

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